1. Species Cocconeis arenicola Riznyk emend. Al-Handal & Riaux-Gob. in Al-Handal et al., 2019
2. Species Cocconeis barleyi T.A.Frankovich & M.De Stefano, 2005
3. Species Cocconeis carinata Riaux-Gobin, Ector & Witkowski
4. Species Cocconeis caulerpacola Witkowski, Car & Dobosz, 2012
5. Species Cocconeis churalis H. Suzuki, 2012
6. Species Cocconeis clandestina A.Schmidt, 1894
7. Species Cocconeis coronatoides Riaux-Gobin & Romero, 2011
8. Species Cocconeis costata Gregory, 1855
9. Species Cocconeis dirupta W.Gregory, 1857
10. Species Cocconeis frustrationis Riaux-Gobin et al., 2015
11. Species Cocconeis gautierii H.F.Van Heurck
12. Species Cocconeis grata A.W.F.Schmidt ex Romero & Riaux-Gobin, 2014
13. Species Cocconeis gregoryi C.Riaux-Gobin, P.Compère & L.Ector, 2014
14. Species Cocconeis heteroidea Hantzsch
15. Species Cocconeis kurakakea Riaux-Gobin & Witkowski, 2018
16. Species Cocconeis magnoareolata Al-Handal, Riaux-Gob., R.Jahn & A.K.Wulff in Al-Handal et al., 2019
17. Species Cocconeis materoxanae M. De Stefano, 2005
18. Species Cocconeis maxima (Grunow) H.Peragallo & M.Peragallo, 1897
19. Species Cocconeis meisteri C.Riaux-Gobin, P.Compère, M.Coste, F.Straub & L.Taxböck, 2014
20. Species Cocconeis molesta Kützing
21. Species Cocconeis nagumoi H.Suzuki, 2006
22. Species Cocconeis napukensis C.Riaux-Gobin, P.Compère, M.Coste, F.Straub & L.Taxböck, 2014
23. Species Cocconeis nosybetiana Riaux-Gobin & Witkowski, 2019
24. Species Cocconeis notata Petit, 1877
25. Species Cocconeis pellucida Hantzsch, 1863
26. Species Cocconeis pelta A.Schmidt, 1874
27. Species Cocconeis pinnata W.Gregory ex Greville, 1859
28. Species Cocconeis placentula Ehrenberg, 1838
29. Species Cocconeis portei E.O'Meara, 1867
30. Species Cocconeis pseudomarginata Gregory, 1857
31. Species Cocconeis sawensis A.Y.Al-Handal & C.Riaux-Gobin, 2014
32. Species Cocconeis scutellum Ehrenberg, 1838
33. Species Cocconeis sijunghoensis R. Jahn & B. M. Suh in Jahn et al., 2020
34. Species Cocconeis singularis Hagelstein, 1939
35. Species Cocconeis spina-christi C.Riaux-Gobin, O.E. Romero, M.Coste & R.Galzin, 2013
36. Species Cocconeis subantarctica Riaux-Gobin & Witkowski, 2017
37. Species Cocconeis subzanskiensis Riaux-Gobin, Witkowski, Ector & Igersheim, 2018
38. Species Cocconeis suzukii C.Riaux-Gobin, P.Compère, M.Coste, F.Straub & L.Taxböck, 2014
39. Species Cocconeis thalassiana O.E.Romero & F.O.López-Fuerte, 2013
40. Species Cocconeis tortilis H.Suzuki, 2014
41. Species Cocconeis tuamotuana Riaux-Gobin et al., 2015
42. Species Cocconeis vrangoensis Al-Handal & Riaux-Gob. in Al-Handal et al., 2019
43. Species Cocconeis coronata Riaux-Gobin & Romero, 2010 accepted as Cocconeis coronatoides Riaux-Gobin & Romero, 2011 (synonym)
44. Species Cocconeis debenedettii Frenguelli & Orlando, 1958 (unaccepted > nomen nudum, invalidly published)
45. Species Cocconeis gautieri van Heurck, 1909 accepted as Cocconeis antiqua J.A.Tempère & J.-J.Brun, 1889 † (synonym)
46. Species Cocconeis imperatrix A.W.F.Schmidt, 1894 accepted as Cocconeis fasciolata (Ehrenberg) N.E.Brown, 1920 accepted as Rhaphoneis fasciolata var. fasciolata Ehrenberg, 1844
47. Species Cocconeis lauriensis J.Frenguelli & H.A.Orlando, 1958 (unaccepted > nomen nudum, invalidly published)
48. Species Cocconeis melchiori Frenguelli & Orlando, 1958 (unaccepted > nomen nudum, invalidly published)
49. Species Cocconeis orbicularis Frenguelli & Orlando, 1958 accepted as Australoneis frenguellii (Riaux-Gobin & J.M.Guerrero) J.M.Guerrero & Riaux-Gobin, 2021 (basionym)
50. Species Cocconeis rudis Frenguelli, 1953 accepted as Planothidium salvadorianum (Hustedt) Lange-Bertalot, 1999 (Taxonomic synonym)
51. Species Cocconeis schuettii van Heurck, 1909 accepted as Cocconeis antiqua J.A.Tempère & J.-J.Brun, 1889 † (synonym)
52. Species Cocconeis splendida Gregory, 1857 accepted as Mastogloia splendida (Gregory) H.Pergallo, 1888 accepted as Cocconeis splendida var. splendida Gregory, 1857 (synonym)
53. Species Cocconeis alucitae Riaux-Gobin & Compère, 2008 (uncertain > unassessed)
54. Species Cocconeis amphiceros Ehrenberg, 1840 (uncertain > unassessed)
55. Species Cocconeis antarctica N.E. Brown, 1920 (uncertain > unassessed)
56. Species Cocconeis arenicola Riznyk, 1973 (uncertain > unassessed)
57. Species Cocconeis borbonica Riaux-Gobin & Compère, 2008 (uncertain > unassessed)
58. Species Cocconeis californica Grunow, 1880 (uncertain > unassessed)
59. Species Cocconeis capensis (Cholnoky) A. Witkowski in A. Witkowski, H. Lange-Bertalot & D. Metzeltin, 2000 accepted as Cocconeis clandestina var. capensis Cholnoky, 1963 (uncertain > unassessed)
60. Species Cocconeis clypeus Ehrenberg, 1838 (uncertain > unassessed)
61. Species Cocconeis communis Heiberg, 1863 (uncertain > unassessed)
62. Species Cocconeis convexa M.H.Giffen, 1967 (uncertain > unassessed)
63. Species Cocconeis coralliensis Riaux-Gobin & Compère, 2008 (uncertain > unassessed)
64. Species Cocconeis curiosa Hustedt, 1958 (uncertain > unassessed)
65. Species Cocconeis dallmannii Al-Handal, Riaux-Gobin, Romero & Wulff, 2008 (uncertain > unassessed)
66. Species Cocconeis dilatata T.Marsson, 1900 (uncertain > unassessed)
67. Species Cocconeis diruptoides Hustedt, 1959 (uncertain > unassessed)
68. Species Cocconeis discrepans A.W.F.Schmidt, 1894 accepted as Amphicocconeis discrepans (A.W.F. Schmidt, 1894) Riaux-Gobin, Witkowski, Ector & Igersheim in Riaux-Gobin et al., 2018 (uncertain > unassessed)
69. Species Cocconeis disculoides Hustedt, 1955 (uncertain > unassessed)
70. Species Cocconeis distans W.Gregory, 1855 (uncertain > unassessed)
71. Species Cocconeis elongata Ehrenberg, 1841 (uncertain > unassessed)
72. Species Cocconeis fasciolata (Ehrenberg) N.E.Brown, 1920 accepted as Rhaphoneis fasciolata var. fasciolata Ehrenberg, 1844 (uncertain > unassessed)
73. Species Cocconeis finnmarchica Grunow, 1880 (uncertain > unassessed)
74. Species Cocconeis germainii Riaux-Gobin, C.; Witkowski, A. & Romero, O.E., 2007 (uncertain > unassessed)
75. Species Cocconeis granulata Grunow, 1877-1882 (uncertain > unassessed)
76. Species Cocconeis granulifera Greville, 1861 (uncertain > unassessed)
77. Species Cocconeis grevillei W.Smith, 1853 (uncertain > unassessed)
78. Species Cocconeis heydrichii H.F.Van Heurck, 1909 (uncertain > unassessed)
79. Species Cocconeis infirmata Manguin, 1957 (uncertain > unassessed)
80. Species Cocconeis interrupta Grunow, 1863 (uncertain > unassessed)
81. Species Cocconeis japonica A.Schmidt, 1874 (uncertain > unassessed)
82. Species Cocconeis krammeri Lange-Bertalot & Metzeltin, 1996 (uncertain > unassessed)
83. Species Cocconeis litigiosa van Heurck, 1909 (uncertain > unassessed)
84. Species Cocconeis marginata Kützing, 1844 (uncertain > unassessed)
85. Species Cocconeis mascarenica Riaux-Gobin & Compère, 2008 (uncertain > unassessed)
86. Species Cocconeis melchioroides Al-Handal, Riaux-Gobin, Romero & Wulff, 2008 (uncertain > unassessed)
87. Species Cocconeis mormonum Ehrenberg, 1871 (uncertain > unassessed)
88. Species Cocconeis neodiminuta Krammer, 1990 (uncertain > unassessed)
89. Species Cocconeis neothumensis Krammer, 1991 (uncertain > unassessed)
90. Species Cocconeis nummularia (Greville) H.Peragallo & M.Peragallo, 1897 accepted as Navicula nummularia Greville, 1859 (uncertain > unassessed)
91. Species Cocconeis pacifica Grunow, 1867 (uncertain > unassessed)
92. Species Cocconeis peltoides Hustedt, 1939 (uncertain > unassessed)
93. Species Cocconeis pinnata (Hustedt) Cleve-Euler, 1934 accepted as Achnanthes pinnata var. pinnata Hustedt, 1922 (uncertain > unassessed)
94. Species Cocconeis pottercovei A.Y.Al-Handal, C.Riaux-Gobin & A.Wulff, 2010 (uncertain > unassessed)
95. Species Cocconeis problematica Van Landingham, 1967 (uncertain > unassessed)
96. Species Cocconeis pseudograta Hustedt, 1939 (uncertain > unassessed)
97. Species Cocconeis pseudonotata M.De Stefano & D.Marino, 2001 (uncertain > unassessed)
98. Species Cocconeis pumila Kützing, 1844 (uncertain > unassessed)
99. Species Cocconeis punctata Ehrenberg, 1841 (uncertain > unassessed)
100. Species Cocconeis quarnerensis (Grunow) A.Schmidt, 1874 (uncertain > unassessed)
101. Species Cocconeis regalis Greville, 1859 (uncertain > unassessed)
102. Species Cocconeis stauroneiformis (W.Smith) H.Okuno, 1957 accepted as Cocconeis scutellum f. stauroneiformis Rabenhorst, 1864 (uncertain > unassessed)
103. Species Cocconeis tenuistriata Lin & Chin, 1980 (uncertain > unassessed)
104. Species Cocconeis villosa H.Peragallo, 1888 (uncertain > unassessed)

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